ggetlisted

# gget Use this skill when a task needs quick bioinformatics lookup across genomic reference databases with the `gget` CLI or Python package. ## When to Use - Finding Ensembl IDs, gene metadata, transcript details, or sequences - Running quick BLAST or BLAT lookups without building a full local pipeline - Fetching reference genome links and annotations from Ensembl - Querying protein structure, pathway, cancer, expression, or disease-association modules through a single interface Use a dedicated workflow instead when the task requires regulated clinical interpretation, high-throughput production pipelines, or fine-grained control over database versions and local indexes. ## Installation Use a clean Python environment. The upstream databases queried by `gget` change over time — upgrade and re-check module docs before relying on an older environment. ```bash python -m venv .venv . .venv/bin/activate python -m pip install --upgrade gget gget --help # or with uv uv venv && . .venv/bin/activate && uv pip install gget ``` ## Basic Patterns ```bash gget <module> [arguments] [options] ``` ```python import gget result = gget.search(["BRCA1"], species="human") ``` ## Common Modules - `gget search`: find Ensembl IDs from search terms - `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs - `gget seq`: fetch nucleotide or amino-acid sequences - `gget ref`: retrieve reference genome download links - `gget blast`: run a quick BLAST query - `gget blat`: locate a